Prenatal screening and diagnosis of fetal aneuploidies, such as trisomy 21 (T21), is an established part of modern obstetrics care. Conventional prenatal screening is built on parameters such as maternal age, sonographic and biochemical markers [1]. Since these parameters are mainly based on phenotypic features, which are essentially epiphenomena associated with the core molecular pathology, their diagnostic performance is usually suboptimal. Pregnancies stratified as high risk by the above screening approaches require further investigation of fetal genetic materials obtained via invasive procedures, such as chorionic villus sampling (CVS) and amniocentesis. These latter procedures carry small, but definite, risk of miscarriage [2]. The demonstration of fetal DNA in maternal plasma in 1997 has opened up possibilities for noninvasive prenatal diagnosis (NIPD) [3].
Maternal plasma DNA contains a mixture of fragmented maternal and fetal genomic DNA [4]. The large background of maternal DNA represents a challenge for the interrogation of fetal chromosomal status. Early studies for NIPD of T21 were polymorphism-based, requiring the measurements of allelic ratios and comparing them with the expected normal values [5-7]. These early methods were based on fetal-specific molecular signatures such as DNA methylation markers [5] and RNA markers [6], or required one to increase the fractional fetal DNA concentration to a sufficiently high level such as using formaldehyde treatment of maternal plasma [7]. However, for the last approach, there are controversies on the effectiveness of formaldehyde treatment because this method could not be replicated consistently by different groups [8-10]. Therefore, the clinical applicability of such a method remains unclear.
It is therefore desirable to provide new techniques for noninvasive prenatal diagnosis using allelic ratios.